Thucydides isn't easy, so don't be embarrased about not understanding everything.
I cheated and looked at a translation to get a sense for how the sentence goes together; this can be useful for reconstructing the meaning of the Greek.
1) What is the substantive that goes with οἱ?
"οἱ δὲ" can be used simply to mean "they"
2) What is τε doing?
3) What is καὶ doing here before a relative pronoun?
τε...καὶ acts as a single unit. I'm not going to try to defend Thucydides sentence structure, but basically I think he's using it to separate ἐξελέξαντο...ὡς ἑκατόν from what comes before it.
4) What is the substantive for τὰ?
Again, there isn't one. It's being used to make a substantive out of a prepositional phrase. τὰ πρὸς τοὺς Ἀθηναίους ἄνδρας = the matters regarding the Athenians (translate this more precisely according to context)
For ὡς ἑκατόν, see the LSJ entry for ὡς, section E:
ὡς with numerals marks that they are to be taken only as a round number, as it were, about, nearly
5) Does the last ὡς just mean "when"?
I would interpret it as a introducing a result clause - the people gave a vote so that/with the result that
they were condemned...
6) ἐς ὀλιγαρχίαν τὰ μάλιστα has got me confused. What is going on here
It seems τὰ μάλιστα can have the meaning "to the highest degree" (LSJ entry for μάλα, section A.III.2)